PhenoSwitch Bioscience is now Allumiqs.
ProTrap HT 96-Well Plate

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High Throughput Precipitation with the ProTrap HT

by Jessica Nickerson, R&D Scientist at Allumiqs

As proteomics moves forward at a rapid pace, so must the sample prep tools that support our workflows.  At Allumiqs we’re committed to helping researchers reimagine organic solvent precipitation-based workflows to afford maximized recovery and surfactant depletion for robust recovery of a proteome sample.  In previous blog posts, we’ve covered the development of the ProTrap XG filtration cartridge by Dr. Alan Doucette’s research group (I’m a former member of this group) to facilitate and simplify organic solvent-based protein precipitation. While our research in the Doucette Lab accelerated the critical precipitation step, now the product team at Allumiqs is elevating our sample prep tools with the new ProTrap HT filter plate to meet customer needs for large-scale and routine preparations which demand further reductions in sample handling and semi- and fully-automated workflows.

Hands-free Sample Prep!

We are excited about applying our methodologies to a new high-throughput format with our 96-well filter plates and equipping customers with this new level of sample prep. While the spin cartridge took the technical guesswork out of isolating your protein pellet, the new filter plate allows complete automation, minimizing technical variabilities associated with sample preparation. The filter plate is highly versatile and compatible with the common A200 workflows. Precipitated protein is recovered either by centrifugation, positive or negative pressure, enabling subsequent on-membrane digestion. Our rigorous validation studies, conducted by our product and mass spec services teams, demonstrated that the filter plate configuration enables the same quantitative recovery, surfactant depletion, and overall reproducibility achieved by the original spin cartridge format.

How low can you go?

Our team set out to optimize protocols for processing approximately 50 µg of starting material, including a customized workflow and reagent kit for serum/plasma preparation.  With this level achieved, we recently began investigating just how low you can go, demonstrating the performance of the filter plate for processing dilute or volume-limited samples. 

Results from a bottom-up preparation of a human mononuclear cell line showed quantitation of 16,-20,000 peptides and 2500-3000 proteins by SWATH MS starting with just 2-10 µg protein. A head-to-head comparison between the filter plate and a conventional vial was done on low starting quantities of CSF. Analysis by bottom-up SWATH MS showed that an automated preparation of as little as 1 µg initial protein in the high-throughput filter plate matched the quantitative precision of a manual precipitation workflow while increasing coverage of the proteome. 

More to come on this at ASMS 2023 in Houston where we’ll be presenting a new poster on more of our findings around low starting material amounts.  Hope to see you there!

Until then I would be happy to chat with you about implementing the new filter plate in your workflow.  Reach out to me anytime at

We’re interested in collaborating with customers like you to advance your research goals. You may require custom protocols and our team would be happy to work with you on that type of initiative.

More info on the ProTrap HT ⬇️ 

For maximum flexibility, we offer our 96-well plates in these packaging configurations:

Cat.No.Product NameDescription
PWP-1001ProTrap HT 96-Well Plates 5PKFive (5) filter plates
PWP-R001ProTrap HT 96-Well Plate + Serum/Plasma ReagentsOne (1) plate with SDS Buffer and Digestion Buffer – a good way to try the plate in your workflow – this is a good one to start with for evaluation, contact to see if your lab qualifies for a complimentary evaluation pack.
PWP-R002ProTrap HT 96-Well Plates 5PK + Serum/Plasma ReagentsFive (5) plates with SDS Buffer and Digestion buffer